annotate qiime2/qiime_diversity_mantel.xml @ 2:51025741f326 draft

Uploaded
author florianbegusch
date Thu, 18 Jul 2019 12:19:15 -0400
parents 370e0b6e9826
children 914fa4daf16a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Apply the Mantel test to two distance matrices</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime diversity mantel
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-dm1=$idm1
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --i-dm2=$idm2
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 #if str($pmethod) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 --p-method=$pmethod
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #if $ppermutations:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 --p-permutations=$ppermutations
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 #if $pintersectids:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 --p-intersect-ids
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 #if str($plabel1):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 --p-label1="$plabel1"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 #if str($plabel2):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 --p-label2="$plabel2"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 --o-visualization=ovisualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36 && cp -r out/* '$ovisualization.files_path'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 && mv '$ovisualization.files_path/index.html' '$ovisualization';
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm1" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm2" optional="False" type="data"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 <param label="--p-method: " name="pmethod" optional="True" type="select">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 <option value="spearman">spearman</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 <option value="pearson">pearson</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="'Distance Matrix 1'"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="'Distance Matrix 2'"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 Apply the Mantel test to two distance matrices
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 ##############################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 Apply a two-sided Mantel test to identify correlation between two distance
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60 matrices. Note: the directionality of the comparison has no bearing on the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 results. Thus, comparing distance matrix X to distance matrix Y is
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 equivalent to comparing Y to X. Note: the order of samples within the two
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 distance matrices does not need to be the same; the distance matrices will
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 be reordered before applying the Mantel test. See the scikit-bio docs for
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65 more details about the Mantel test: http://scikit-
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 dm1 : DistanceMatrix
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 Matrix of distances between pairs of samples.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 dm2 : DistanceMatrix
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 Matrix of distances between pairs of samples.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 method : Str % Choices('spearman', 'pearson'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 The correlation test to be applied in the Mantel test.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 permutations : Int % Range(0, None), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 The number of permutations to be run when computing p-values. Supplying
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 a value of zero will disable permutation testing and p-values will not
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 be calculated (this results in *much* quicker execution time if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 p-values are not desired).
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 intersect_ids : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82 If supplied, IDs that are not found in both distance matrices will be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 discarded before applying the Mantel test. Default behavior is to error
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84 on any mismatched IDs.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 label1 : Str, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 Label for `dm1` in the output visualization.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 label2 : Str, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 Label for `dm2` in the output visualization.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 visualization : Visualization
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
93 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
94 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
97 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
98 </tool>